HEADER SUGAR BINDING PROTEIN 04-SEP-09 3JQ0 TITLE CRYSTAL STRUCTURE OF SUSD SUPERFAMILY PROTEIN (YP_001299712.1) FROM TITLE 2 BACTEROIDES VULGATUS ATCC 8482 AT 1.13 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUSD SUPERFAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE OUTER MEMBRANE PROTEIN, PROBABLY INVOLVED IN COMPND 5 NUTRIENT BINDING; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES VULGATUS ATCC 8482; SOURCE 3 ORGANISM_TAXID: 435590; SOURCE 4 STRAIN: ATCC 8482 / DSM 1447 / NCTC 11154; SOURCE 5 GENE: BVU_2431, YP_001299712.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS YP_001299712.1, SUSD SUPERFAMILY PROTEIN, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, RAGB, SUSD AND HYPOTHETICAL PROTEINS, UNKNOWN FUNCTION, SUGAR KEYWDS 4 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3JQ0 1 REMARK SEQADV REVDAT 4 24-JUL-19 3JQ0 1 REMARK LINK REVDAT 3 01-NOV-17 3JQ0 1 REMARK REVDAT 2 13-JUL-11 3JQ0 1 VERSN REVDAT 1 22-SEP-09 3JQ0 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SUSD SUPERFAMILY PROTEIN JRNL TITL 2 (YP_001299712.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.13 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 187080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9433 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8128 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 454 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3866 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 833 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.08000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.753 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4249 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2936 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5782 ; 1.673 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7142 ; 1.013 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 6.113 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;34.015 ;24.420 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;11.578 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.435 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 582 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4812 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 922 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2483 ; 1.553 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1016 ; 0.732 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4010 ; 2.206 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1766 ; 3.213 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1740 ; 4.421 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7185 ; 1.529 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 861 ; 9.239 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7061 ; 3.897 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS ADJUSTED TO REMARK 3 QUENCH THE DIFFERENCE FOURIER DENSITY. 3. GLYCEROL (GOL), REMARK 3 SULFATE (SO4), CHLORIDE (CL), AND 2-AMINO-2-HYDROXYMETHYL- REMARK 3 PROPANE-1,3-DIOL (TRIS BASE, TRS) MOLECULES FROM THE REMARK 3 CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. REMARK 3 RAMACHANDRAN OUTLIER RESIDUES 66, 69 AND 440 ARE SUPPORTED BY REMARK 3 ELECTRON DENSITY. REMARK 4 REMARK 4 3JQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97936 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT MIRROR, VERTICAL AND REMARK 200 HORIZONTAL FOCUSSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 187091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 29.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : 0.58000 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.60M (NH4)2SO4, 0.1M TRIS PH 8.0, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 215.97733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.98867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 161.98300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.99433 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 269.97167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 215.97733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 107.98867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 53.99433 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 161.98300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 269.97167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A REMARK 300 MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 784 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 GLY A 33 REMARK 465 THR A 34 REMARK 465 ALA A 35 REMARK 465 TYR A 36 REMARK 465 GLY A 165 REMARK 465 GLN A 166 REMARK 465 ASN A 167 REMARK 465 LEU A 168 REMARK 465 ASP A 169 REMARK 465 LEU A 170 REMARK 465 SER A 171 REMARK 465 ASN A 172 REMARK 465 ILE A 173 REMARK 465 THR A 174 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 GLU A 164 CG CD OE1 OE2 REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 LYS A 272 CD CE NZ REMARK 470 LYS A 305 CE NZ REMARK 470 LYS A 518 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 105 O HOH A 840 2.15 REMARK 500 OE2 GLU A 411 O HOH A 725 2.16 REMARK 500 OD1 ASN A 243 O HOH A 613 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MSE A 377 CB MSE A 377 CG -0.204 REMARK 500 GLU A 432 CG GLU A 432 CD 0.128 REMARK 500 GLU A 432 CD GLU A 432 OE1 0.092 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PHE A 90 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 332 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 MSE A 377 CG - SE - CE ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 394 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 66 -59.81 -132.83 REMARK 500 ALA A 69 -141.25 -88.20 REMARK 500 TYR A 202 36.33 -89.08 REMARK 500 GLU A 284 -61.77 -130.19 REMARK 500 PRO A 440 40.71 -107.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396554 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE THIS CONSTRUCT (RESIDUES 33-524) WAS EXPRESSED WITH A REMARK 999 PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3JQ0 A 33 524 UNP A6L326 A6L326_BACV8 33 524 SEQADV 3JQ0 GLY A 0 UNP A6L326 EXPRESSION TAG SEQRES 1 A 493 GLY GLY THR ALA TYR TRP LYS ASN PRO ASP GLN PHE THR SEQRES 2 A 493 ALA PHE ASN THR GLY LEU HIS ALA LEU LEU ARG GLU LYS SEQRES 3 A 493 SER TYR ASN PHE PHE LEU LEU GLY GLU PRO ARG ALA ASP SEQRES 4 A 493 ILE TYR GLY ASP ASN PRO ILE GLY GLY GLU ALA SER GLN SEQRES 5 A 493 GLY MSE GLU ARG LEU PRO PHE ASN THR ILE ASN LYS GLU SEQRES 6 A 493 ASN VAL GLY ILE SER ASN TYR GLY ASP MSE TYR LYS ILE SEQRES 7 A 493 ILE ASN GLN ILE ASN GLN MSE ILE ALA LYS THR THR GLU SEQRES 8 A 493 THR THR ILE LEU THR GLU ALA THR GLN ASN TYR TYR LEU SEQRES 9 A 493 GLY GLU ALA TYR GLY MSE ARG ALA TYR LEU TYR PHE HIS SEQRES 10 A 493 LEU LEU ARG SER TRP GLY ASP VAL VAL LEU TYR LEU ASP SEQRES 11 A 493 TYR THR GLU GLY GLN ASN LEU ASP LEU SER ASN ILE THR SEQRES 12 A 493 LYS GLY VAL SER PRO ALA THR GLU VAL MSE GLU GLN ILE SEQRES 13 A 493 LYS LYS ASP ILE GLN ALA SER GLU ASN ALA PHE GLY SER SEQRES 14 A 493 ASP TYR SER PHE LYS LEU GLY ARG HIS PHE TRP SER ALA SEQRES 15 A 493 ALA ALA THR GLN MSE LEU LYS GLY GLU ALA TYR LEU TRP SEQRES 16 A 493 SER GLY ARG GLN MSE ASN GLY GLY ASN SER ASP TYR THR SEQRES 17 A 493 ILE ALA LYS ASN ALA PHE GLU ASN VAL LYS LYS ALA ASP SEQRES 18 A 493 VAL GLY LEU VAL THR SER SER PHE LYS ASP ILE PHE SER SEQRES 19 A 493 PHE GLU ASN LYS LYS ASN LYS GLU MSE ILE PHE THR ILE SEQRES 20 A 493 HIS ASN GLY LYS ASP GLU TYR GLU MSE TRP GLY GLY TYR SEQRES 21 A 493 TYR ARG MSE ARG LEU ILE PRO ALA GLN ASP LYS MSE VAL SEQRES 22 A 493 LYS ILE TYR CYS ASP GLU ASN GLY ASN SER PHE VAL GLY SEQRES 23 A 493 THR PRO ASP ALA GLN LEU ASN GLY LEU THR GLN LEU GLN SEQRES 24 A 493 VAL ARG ARG GLU PHE TYR PHE LYS GLY PHE ARG ASN ASN SEQRES 25 A 493 ASP THR ARG TRP THR THR SER LEU LYS ALA VAL TYR LYS SEQRES 26 A 493 LYS ASP ALA GLN GLY VAL VAL SER TYR PHE GLY PRO ILE SEQRES 27 A 493 THR TYR LYS PHE GLN GLY THR MSE LEU GLU GLY GLY SER SEQRES 28 A 493 THR ARG SER PHE LEU ASP ASP PHE PRO ILE TYR ARG TYR SEQRES 29 A 493 ALA ASP CYS LEU LEU GLN LEU ALA MSE ALA LYS VAL LEU SEQRES 30 A 493 LEU GLY GLU ASP PRO THR GLU GLU ILE ASN ALA VAL ARG SEQRES 31 A 493 GLU ARG ALA TYR GLY SER LYS TYR PHE ASN GLU HIS LYS SEQRES 32 A 493 ALA GLU ILE ALA TYR PRO ASN ASP ASN ASP PRO GLU PHE SEQRES 33 A 493 TYR THR ASP ASN LYS TRP MSE LYS PRO ASP ASN ALA GLY SEQRES 34 A 493 ALA LEU GLU ALA ILE LEU LYS GLU ARG LEU ARG GLU PHE SEQRES 35 A 493 MSE PHE GLU GLY LYS ARG TRP TYR ASP ILE ARG LEU LEU SEQRES 36 A 493 GLY TRP ASP TYR VAL HIS GLN TYR SER SER ALA GLU GLN SEQRES 37 A 493 SER ARG LEU LEU TRP PRO ILE ASP ALA GLY THR LEU THR SEQRES 38 A 493 ASN ASN SER ALA LEU LYS GLN THR PRO GLY TYR GLU MODRES 3JQ0 MSE A 85 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 106 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 116 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 141 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 184 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 218 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 231 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 274 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 287 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 294 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 303 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 377 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 404 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 454 MET SELENOMETHIONINE MODRES 3JQ0 MSE A 474 MET SELENOMETHIONINE HET MSE A 85 8 HET MSE A 106 8 HET MSE A 116 8 HET MSE A 141 13 HET MSE A 184 8 HET MSE A 218 8 HET MSE A 231 13 HET MSE A 274 8 HET MSE A 287 13 HET MSE A 294 8 HET MSE A 303 8 HET MSE A 377 8 HET MSE A 404 18 HET MSE A 454 8 HET MSE A 474 8 HET TRS A 1 8 HET GOL A 2 12 HET GOL A 3 6 HET GOL A 4 6 HET GOL A 5 6 HET SO4 A 6 5 HET SO4 A 7 10 HET SO4 A 8 5 HET CL A 9 1 HETNAM MSE SELENOMETHIONINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 CL CL 1- FORMUL 11 HOH *833(H2 O) HELIX 1 1 ASN A 39 LYS A 57 1 19 HELIX 2 2 LYS A 57 GLU A 66 1 10 HELIX 3 3 GLY A 84 LEU A 88 5 5 HELIX 4 4 SER A 101 GLY A 104 5 4 HELIX 5 5 ASP A 105 THR A 123 1 19 HELIX 6 6 THR A 127 GLY A 154 1 28 HELIX 7 7 PRO A 179 GLY A 199 1 21 HELIX 8 8 SER A 212 MSE A 231 1 20 HELIX 9 9 GLY A 234 LYS A 249 1 16 HELIX 10 10 SER A 259 SER A 265 1 7 HELIX 11 11 PHE A 266 LYS A 269 5 4 HELIX 12 12 GLU A 286 TYR A 291 5 6 HELIX 13 13 TYR A 292 ILE A 297 1 6 HELIX 14 14 ALA A 299 ILE A 306 1 8 HELIX 15 15 THR A 318 LEU A 323 5 6 HELIX 16 16 ARG A 333 LYS A 338 5 6 HELIX 17 17 THR A 345 SER A 350 1 6 HELIX 18 18 TYR A 395 LEU A 409 1 15 HELIX 19 19 PRO A 413 GLY A 426 1 14 HELIX 20 20 GLY A 426 HIS A 433 1 8 HELIX 21 21 HIS A 433 ALA A 438 1 6 HELIX 22 22 ASP A 444 THR A 449 1 6 HELIX 23 23 PRO A 456 ALA A 459 5 4 HELIX 24 24 GLY A 460 PHE A 473 1 14 HELIX 25 25 LYS A 478 GLY A 487 1 10 HELIX 26 26 GLY A 487 SER A 495 1 9 HELIX 27 27 GLU A 498 LEU A 502 5 5 HELIX 28 28 ASP A 507 ASN A 514 1 8 SHEET 1 A 2 TYR A 72 ASP A 74 0 SHEET 2 A 2 GLN A 330 VAL A 331 -1 O GLN A 330 N ASP A 74 SHEET 1 B 2 MSE A 274 ILE A 278 0 SHEET 2 B 2 PHE A 390 ARG A 394 -1 O PHE A 390 N ILE A 278 SHEET 1 C 2 LEU A 351 LYS A 357 0 SHEET 2 C 2 VAL A 363 THR A 370 -1 O GLY A 367 N VAL A 354 LINK C GLY A 84 N MSE A 85 1555 1555 1.34 LINK C MSE A 85 N GLU A 86 1555 1555 1.33 LINK C ASP A 105 N MSE A 106 1555 1555 1.33 LINK C MSE A 106 N TYR A 107 1555 1555 1.33 LINK C GLN A 115 N MSE A 116 1555 1555 1.34 LINK C MSE A 116 N ILE A 117 1555 1555 1.34 LINK C GLY A 140 N MSE A 141 1555 1555 1.35 LINK C MSE A 141 N ARG A 142 1555 1555 1.33 LINK C VAL A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N GLU A 185 1555 1555 1.33 LINK C GLN A 217 N MSE A 218 1555 1555 1.35 LINK C MSE A 218 N LEU A 219 1555 1555 1.32 LINK C GLN A 230 N MSE A 231 1555 1555 1.33 LINK C MSE A 231 N ASN A 232 1555 1555 1.33 LINK C GLU A 273 N MSE A 274 1555 1555 1.32 LINK C MSE A 274 N ILE A 275 1555 1555 1.33 LINK C GLU A 286 N MSE A 287 1555 1555 1.33 LINK C MSE A 287 N TRP A 288 1555 1555 1.34 LINK C ARG A 293 N MSE A 294 1555 1555 1.34 LINK C MSE A 294 N ARG A 295 1555 1555 1.33 LINK C LYS A 302 N MSE A 303 1555 1555 1.33 LINK C MSE A 303 N VAL A 304 1555 1555 1.33 LINK C THR A 376 N MSE A 377 1555 1555 1.33 LINK C MSE A 377 N LEU A 378 1555 1555 1.32 LINK C ALA A 403 N MSE A 404 1555 1555 1.33 LINK C MSE A 404 N ALA A 405 1555 1555 1.34 LINK C TRP A 453 N MSE A 454 1555 1555 1.33 LINK C MSE A 454 N LYS A 455 1555 1555 1.32 LINK C PHE A 473 N MSE A 474 1555 1555 1.34 LINK C MSE A 474 N PHE A 475 1555 1555 1.35 CISPEP 1 TYR A 439 PRO A 440 0 9.69 SITE 1 AC1 9 PHE A 204 ARG A 208 ASP A 252 LYS A 270 SITE 2 AC1 9 HOH A 562 HOH A 606 HOH A 851 HOH A 957 SITE 3 AC1 9 HOH A1333 SITE 1 AC2 7 ASN A 94 LYS A 95 ARG A 501 HOH A 673 SITE 2 AC2 7 HOH A 731 HOH A 912 HOH A1220 SITE 1 AC3 11 HIS A 51 ALA A 52 ARG A 55 HIS A 209 SITE 2 AC3 11 PHE A 210 THR A 277 ILE A 278 HIS A 279 SITE 3 AC3 11 HOH A 604 HOH A 821 HOH A1117 SITE 1 AC4 7 SER A 364 TYR A 365 HOH A 713 HOH A 800 SITE 2 AC4 7 HOH A 810 HOH A1123 HOH A1173 SITE 1 AC5 6 TYR A 336 TRP A 347 HOH A 598 HOH A 686 SITE 2 AC5 6 HOH A 778 HOH A1023 SITE 1 AC6 10 GLN A 230 GLY A 487 TRP A 488 HOH A 720 SITE 2 AC6 10 HOH A 837 HOH A 845 HOH A 949 HOH A1003 SITE 3 AC6 10 HOH A1070 HOH A1216 SITE 1 AC7 9 GLY A 381 SER A 382 THR A 383 HOH A 718 SITE 2 AC7 9 HOH A 724 HOH A 735 HOH A 741 HOH A 746 SITE 3 AC7 9 HOH A 754 SITE 1 AC8 6 ARG A 341 ASN A 342 HOH A 529 HOH A 809 SITE 2 AC8 6 HOH A 868 HOH A1140 SITE 1 AC9 3 ARG A 341 ASN A 342 HOH A 868 CRYST1 75.804 75.804 323.966 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013192 0.007616 0.000000 0.00000 SCALE2 0.000000 0.015233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003087 0.00000